Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009096.1 Kokia drynarioides strain JFW-HI SEQ_123797, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24067
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:12189 original size:2 final size:2
Alignment explanation
Indices: 12184--12216 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12174 GATATATATA
12184 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12217 ATGCAAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:15118 original size:2 final size:2
Alignment explanation
Indices: 15113--15159 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
15103 TATTTTATTT
15113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15155 TA TA T
1 TA TA T
15160 TACCATTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16415 original size:2 final size:2
Alignment explanation
Indices: 16408--16439 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16398 GGGTAAGATA
*
16408 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16440 GTATGTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16440 original size:8 final size:8
Alignment explanation
Indices: 16409--16459 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
16399 GGTAAGATAA
*
16409 TATATATA
1 TATATATG
*
16417 TATATATA
1 TATATATG
16425 TATATATG
1 TATATATG
16433 TATATATG
1 TATATATG
*
16441 TATGTATG
1 TATATATG
*
16449 TATGTATG
1 TATATATG
16457 TAT
1 TAT
16460 GGACCATGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:16444 original size:4 final size:4
Alignment explanation
Indices: 16429--16460 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
16419 TATATATATA
*
16429 TATG TATA TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG
16461 GACCATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:16444 original size:12 final size:12
Alignment explanation
Indices: 16409--16459 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
16399 GGTAAGATAA
*
16409 TATATATATATA
1 TATATATATATG
16421 TATATATATATG
1 TATATATATATG
*
16433 TATATATGTATG
1 TATATATATATG
* *
16445 TATGTATGTATG
1 TATATATATATG
16457 TAT
1 TAT
16460 GGACCATGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:19988 original size:6 final size:6
Alignment explanation
Indices: 19979--20009 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
19969 TGCTGAGGCT
*
19979 GAGCTA GAGCCA GAGCCA GAGCCA GAGCCA G
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA G
20010 CAGCAGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.29, G:0.35, T:0.03
Consensus pattern (6 bp):
GAGCCA
Found at i:21968 original size:22 final size:20
Alignment explanation
Indices: 21935--21974 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
21925 ATTATTTTAA
*
21935 TAAAATTTTAATACATTTTT
1 TAAAATTTTAATAAATTTTT
21955 TAAATATTTATAATAAATTT
1 TAAA-ATTT-TAATAAATTT
21975 AATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATTTTAATAAATTTTT
Found at i:21987 original size:20 final size:20
Alignment explanation
Indices: 21911--21988 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
21901 TTACATGATC
* * *
21911 TTAATATTATTATAATTATT
1 TTAATAATATTATAATAAAT
* * *
21931 TTAATAAAATTTTAATACAT
1 TTAATAATATTATAATAAAT
**
21951 TTTTTAAATATTTATAATAAAT
1 TTAAT-AATA-TTATAATAAAT
21973 TTAATAATATTATAAT
1 TTAATAATATTATAAT
21989 TGTTTTTTGA
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
20 24 0.56
21 7 0.16
22 12 0.28
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATAATATTATAATAAAT
Found at i:23307 original size:22 final size:22
Alignment explanation
Indices: 23262--23335 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 22
23252 GAAACAGTAA
*
23262 GCACACACAGTGCAATCCAATAG
1 GCACACATAGTGCAAT-CAATAG
23285 GCACACATAGTGCAATCAATAG
1 GCACACATAGTGCAATCAATAG
* * * *
23307 GCGCACATAGCGCAAATCAGTAA
1 GCACACATAGTGC-AATCAATAG
23330 GCACAC
1 GCACAC
23336 GAAGTGCGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.39
23 27 0.61
ACGTcount: A:0.39, C:0.28, G:0.19, T:0.14
Consensus pattern (22 bp):
GCACACATAGTGCAATCAATAG
Done.